ABSTRACT: The impacts of the El Niño Southern Oscillation (ENSO) and the Pacific Decadal Oscillation (PDO) on the ecology of the northeast Pacific are well known. However, recently there has been a shift in the dominance of El Niño events from the eastern Pacific (canonical) El Niño, to the central Pacific (Modoki) El Niño, concurrent with a strengthening of the North Pacific Gyre Oscillation (NPGO). Our examination of ocean conditions and seabird reproductive success in central California shows that the way these physical factors affect the pelagic food web is also changing. Reproduction of Cassin’s auklet Ptycoramphus aleuticus and Brandt’s cormorant Phalacrocorax penicillatus, species that forage at different trophic levels, responded primarily to ENSO variability from the 1970s to the 1990s. By 1995, however, NPGO had become the dominant variable determining Cassin’s auklet reproductive success. Eventually, NPGO also became correlated with Brandt’s cormorant success but in the opposite direction to Cassin’s auklet. Thus, during the mid-1990s, the correlation between the reproduction of these 2 species weakened and eventually became inversely correlated. This shift from coherent reproduction, presumably bottom-up driven, to an inverse relationship between the 2 species suggests that the structure of the local marine food web changed as the equatorial forcing changed. This non-stationary response of seabirds to physical forcing is cause for concern since predictions of future ecosystem productivity and effects of climate change rely on the assumption that a species’ response to environmental conditions is consistent over time.